SARS-CoV-2 ARTIC Sequencing report

Results generated through the wf-artic Nextflow workflow provided by Oxford Nanopore Technologies.

Read Quality control

This section displays basic QC metrics indicating read data quality.

Artic Analysis status

The panel below lists samples which failed to produce results from the primary ARTIC analysis. Samples not listed here were analysed successfully, but may still contain inconclusive or invalid results. See the following sections for further indications of failed or inconclusive results.

All samples analysed successfully

Genome coverage

Plots below indicate depth of coverage from data used within the Artic analysis coloured by amplicon pool. Variant filtering during the ARTIC analysis mandates a minimum coverage of at least 20X at variant/genotyping loci for a call to be made.

NB: To better display all possible data, the depth axes of the plots below are not tied between plots for different samples. Care should be taken in comparing depth across samples.

Variant call summaries

The following tables and figures are derived from the output of bcftools stats.

Variant counts:

sample MNPs SNPs indels multiallelic SNP sites multiallelic sites no-ALTs others records
Magmax.pass.named.stats 0 0 0 0 0 0 0 0
Magmax10.pass.named.stats 0 13 0 0 0 0 0 13
Magmax2.pass.named.stats 0 0 0 0 0 0 0 0
Magmax3.pass.named.stats 0 1 0 0 0 0 0 1
Magmax4.pass.named.stats 0 8 0 0 0 0 0 8
Magmax5.pass.named.stats 0 14 0 0 0 0 0 14
Magmax6.pass.named.stats 0 14 0 0 0 0 0 14
Magmax7.pass.named.stats 0 5 0 0 0 0 0 5
Magmax8.pass.named.stats 1 7 0 0 0 0 0 8
Magmax9.pass.named.stats 0 8 0 0 0 0 0 8
NanoTrap1.pass.named.stats 0 22 0 0 0 0 0 22
NanoTrap10.pass.named.stats 0 22 0 0 0 0 0 22
NanoTrap2.pass.named.stats 0 10 0 0 0 0 0 10
NanoTrap3.pass.named.stats 0 16 0 0 0 0 0 16
NanoTrap4.pass.named.stats 0 9 0 0 0 0 0 9
NanoTrap5.pass.named.stats 0 14 0 0 0 0 0 14
NanoTrap6.pass.named.stats 0 15 0 0 0 0 0 15
NanoTrap7.pass.named.stats 0 15 0 0 0 0 0 15
NanoTrap8.pass.named.stats 0 24 0 0 0 0 0 24
NanoTrap9.pass.named.stats 0 24 0 0 0 0 0 24

Transitions and tranversions:

sample ts tv ts/tv ts (1st ALT) tv (1st ALT) ts/tv (1st ALT)
Magmax.pass.named.stats 0 0 0.00 0 0 0.00
Magmax10.pass.named.stats 9 4 2.25 9 4 2.25
Magmax2.pass.named.stats 0 0 0.00 0 0 0.00
Magmax3.pass.named.stats 1 0 0.00 1 0 0.00
Magmax4.pass.named.stats 7 1 7.00 7 1 7.00
Magmax5.pass.named.stats 7 7 1.00 7 7 1.00
Magmax6.pass.named.stats 7 7 1.00 7 7 1.00
Magmax7.pass.named.stats 1 4 0.25 1 4 0.25
Magmax8.pass.named.stats 6 1 6.00 6 1 6.00
Magmax9.pass.named.stats 7 1 7.00 7 1 7.00
NanoTrap1.pass.named.stats 16 6 2.67 16 6 2.67
NanoTrap10.pass.named.stats 19 3 6.33 19 3 6.33
NanoTrap2.pass.named.stats 8 2 4.00 8 2 4.00
NanoTrap3.pass.named.stats 14 2 7.00 14 2 7.00
NanoTrap4.pass.named.stats 9 0 0.00 9 0 0.00
NanoTrap5.pass.named.stats 7 7 1.00 7 7 1.00
NanoTrap6.pass.named.stats 7 8 0.88 7 8 0.88
NanoTrap7.pass.named.stats 7 8 0.88 7 8 0.88
NanoTrap8.pass.named.stats 17 7 2.43 17 7 2.43
NanoTrap9.pass.named.stats 17 7 2.43 17 7 2.43

Substitution types

Base substitutions aggregated across all samples (symmetrised by pairing)

Indel lengths

Insertion and deletion lengths aggregated across all samples.

No indels to report.

NextClade analysis

The following view is produced by the nextclade software.

The table shows errors, warnings or failed genes per sample:

Sample Name errors warnings failed genes
Magmax MN908947.3 Unable to align: no seed matches None <<ALL>>
Magmax10 MN908947.3 None None None
Magmax2 MN908947.3 Unable to align: no seed matches None <<ALL>>
Magmax3 MN908947.3 None None None
Magmax4 MN908947.3 None None None
Magmax5 MN908947.3 None None None
Magmax6 MN908947.3 None None None
Magmax7 MN908947.3 None None None
Magmax8 MN908947.3 None None None
Magmax9 MN908947.3 None None None
NanoTrap1 MN908947.3 None None None
NanoTrap10 MN908947.3 None None None
NanoTrap2 MN908947.3 None None None
NanoTrap3 MN908947.3 None None None
NanoTrap4 MN908947.3 None None None
NanoTrap5 MN908947.3 None None None
NanoTrap6 MN908947.3 None None None
NanoTrap7 MN908947.3 None None None
NanoTrap8 MN908947.3 None None None
NanoTrap9 MN908947.3 None None None

Note: For targeted sequencing, such as SpikeSeq, Nextclade may report 'Missing data' QC fails. This is expected and not a concern provided the regions of interest are not reported as missing.

Lineage

The table below reports the lineage of each sample as calculated by pangolin.

taxon lineage conflict ambiguity_score scorpio_call scorpio_support scorpio_conflict version pangolin_version pangoLEARN_version pango_version status note
Magmax4_MN908947.3 B.1.567 0.0 0.692374 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
Magmax5_MN908947.3 B.1.126 0.0 0.905324 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
Magmax6_MN908947.3 B.1.126 0.0 0.874690 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap1_MN908947.3 B.1.429 0.0 0.807975 Epsilon (B.1.429-like) 0.9286 0.0 PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc scorpio call: Alt alleles 13; Ref alleles 0; Amb alleles 1; Oth alleles 0
NanoTrap10_MN908947.3 B.1.2 0.0 0.952030 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap2_MN908947.3 B.1.243 0.0 0.786973 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap3_MN908947.3 B.1.241 0.0 0.833376 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap4_MN908947.3 B.1 0.0 0.835767 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap5_MN908947.3 B.1.126 0.0 0.925514 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap6_MN908947.3 B.1 0.0 0.922457 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap7_MN908947.3 B.1.126 0.0 0.939557 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap8_MN908947.3 B.1.2 0.0 1.000000 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
NanoTrap9_MN908947.3 B.1.2 0.0 0.976577 NaN NaN NaN PLEARN-v1.2.105 3.1.17 2021-12-06 v1.2.105 passed_qc NaN
Magmax_MN908947.3 None NaN NaN NaN NaN NaN PANGO-v1.2.105 3.1.17 2021-12-06 v1.2.105 fail N_content:1.0
Magmax10_MN908947.3 None NaN NaN NaN NaN NaN PANGO-v1.2.105 3.1.17 2021-12-06 v1.2.105 fail N_content:0.47
Magmax2_MN908947.3 None NaN NaN NaN NaN NaN PANGO-v1.2.105 3.1.17 2021-12-06 v1.2.105 fail N_content:1.0
Magmax3_MN908947.3 None NaN NaN NaN NaN NaN PANGO-v1.2.105 3.1.17 2021-12-06 v1.2.105 fail N_content:0.98
Magmax7_MN908947.3 None NaN NaN NaN NaN NaN PANGO-v1.2.105 3.1.17 2021-12-06 v1.2.105 fail N_content:0.81
Magmax8_MN908947.3 None NaN NaN NaN NaN NaN PANGO-v1.2.105 3.1.17 2021-12-06 v1.2.105 fail N_content:0.59
Magmax9_MN908947.3 None NaN NaN NaN NaN NaN PANGO-v1.2.105 3.1.17 2021-12-06 v1.2.105 fail N_content:0.74

Software versions

The table below highlights versions of key software used within the analysis.

Name Version
medaka 1.4.3
minimap2 2.18-r1015
bcftools 1.12
samtools 1.12
nextclade 1.5.1
artic 1.3.0
pangolin 3.1.17
pangolearn 2021-12-06
constellations v0.1.1
scorpio 0.3.16
pango-designation used by pangoLEARN/Usher v1.2.105
pango-designation aliases 1.2.117

Workflow parameters

The table below highlights values of the main parameters used in this analysis.

Key Value
help False
out_dir /home/ceres_bio/fastout/output5
fastq /home/ceres_bio/fastin/input5/preprint1/samples
sanitize_fastq False
samples /home/ceres_bio/fastin/input5/preprint1/sample_sheet/sample_sheet1
report_depth 100
medaka_model r941_prom_variant_g360
scheme_name SARS-CoV-2
scheme_version V3
genotype_variants None
report_clade True
report_lineage True
report_coverage True
report_variant_summary True
report_detailed False
wfversion v0.3.6
pangolin_version 3.1.16
aws_image_prefix None
aws_queue None
lab_id None
testkit None
report_name report
monochrome_logs False
validate_params True
show_hidden_params False
schema_ignore_params show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,pangolin_version,wfversion
_min_len 400
_max_len 700
_max_softclip_length 0
full_scheme_name SARS-CoV-2/V3

About

This report was produced using the epi2me-labs/wf-artic. The workflow can be run using nextflow epi2me-labs/wf-artic --help

Version details Revision: master Git Commit: 49861c8e4f6e017bb3b534a946b63518aa300b05

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